使用 Homebrew, apt, Nix 安装 spades

项目链接

• 主页
• 仓库

命令和别名

• coronaspades.py
• metaplasmidspades.py
• metaspades.py
• metaviralspades.py
• plasmidspades.py
• rnaspades.py
• rnaviralspades.py
• spades-bwa
• spades-convert-bin-to-fasta
• spades-core
• spades-corrector-core
• spades-gbuilder
• spades-gfa-split
• spades-gmapper
• spades-gsimplifier
• spades-hammer
• spades-ionhammer
• spades-kmer-estimating
• spades-kmercount
• spades-read-filter
• spades.py
• spades_init.py

项目历史

The SPAdes project traces its cited work back to the 2012 and 2013 SPAdes papers, and the current official repository was created on GitHub in 2016. Its README presents SPAdes as a toolkit for assembly and analysis of sequencing data, primarily Illumina data, with support for IonTorrent and hybrid modes using long reads as supplementary data.

采用历史

SPAdes accumulated specialized pipelines around common genomics workflows, including metaSPAdes, plasmidSPAdes, metaviralSPAdes, rnaSPAdes, and coronaSPAdes. The official citation guidance lists papers for these modes, reflecting adoption across bacterial, metagenomic, viral, transcriptomic, plasmid, and public-health sequencing use cases.

使用方式

Users usually run `spades.py` or one of the mode-specific wrappers with input read files and an output directory, then inspect generated assemblies and logs. The package also ships standalone utilities for k-mer counting, graph operations, sequence-to-graph alignment, and related assembly tasks.

为什么软件包爱好者会关心

SPAdes is a good example of why scientific CLIs get packaged broadly: it has compiled code, Python entry points, test commands, large release artifacts, and many subcommands that researchers want to install through Homebrew, Debian/Ubuntu, Nix, or other reproducible environments instead of hand-building each lab machine.

时间线

• 2012: Early SPAdes paper cited by the official project.
• 2013: Additional early SPAdes paper cited by the official project.
• 2016: Current public GitHub repository created.
• 2017: metaSPAdes paper listed in official citation guidance.
• 2022: coronaSPAdes paper listed in official citation guidance.

Related projects

• Related SPAdes modes and pipelines include metaSPAdes, plasmidSPAdes, metaviralSPAdes, rnaSPAdes, biosyntheticSPAdes, coronaSPAdes, and SPlitteR.

来源

• https://ablab.github.io/spades/
• https://ablab.github.io/spades/citation.html
• https://api.github.com/repos/ablab/spades
• https://github.com/ablab/spades
• input.source_facts.package-manager